You should definitely be using strict and warnings, for starters.

Next, do you really intend to update 

           $hash{$Query}[3] = $one;
           $hash{$Query}[4] = $two;

[download]
in all 4 blocks? That seems strange.

If you didn't intend that, what I'd suggest is modifying your code to simplify things - it would also make debugging simpler. 

while (<FH>) {
   my ($Query, $Score, $Start, $End, $one, $two) = split;
   my $aref=[$Score, $Start, $End, $one, $two];

   if ( ! exists ( $hash{$Query} ) ) {
      $hash{$Query} = $aref;
   }
   else {
      if ( $hash{$Query}[1] > $Start ) {
           $hash{$Query} = $aref;
      }
   }
   if ( ! exists ( $hash2{$Query} ) ) {
      $hash2{$Query}= $aref;
   }
   else {
      if ( $hash2{$Query}[2] < $End ) {
           $hash2{$Query} = $aref;
      }
   }
}

[download]
That might make things a bit easier to debug...

Mike

In reply to Re: Parsing and Finding Max Min by RMGir
in thread Parsing and Finding Max Min by Perl_Crazy

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